7JPN: Arpin-bound Arp2/3 complex

Cryo-EM structure of Arpin-bound Arp2/3 complex. Determined by electron microscopy at 3.24 Å resolution. Released 9 Feb 2022.

Method: Electron microscopy
Resolution: 3.24 Å
Organisms: Bos taurus, Homo sapiens
Chains: 8
Atoms: 15,040
Mol. weight: 225.82 kDa
Ligands: ATP, MG
Released: 9 Feb 2022

Explore 7JPN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7JPN contains 86 α-helices and 91 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 23 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	29-32	4	1
β-strand	35-37	3	2
α-helix	56-58	3
β-strand	60-62	3	2
α-helix	63-66	4
β-strand	73-75	3	2
β-strand	78-79	2	3
β-strand	82-83	2	3
α-helix	86-95	10
α-helix	96-101	6
β-strand	110-114	5	1
α-helix	120-132	13
β-strand	139-143	5	1
α-helix	144-151	8
α-helix	152-154	3
β-strand	165-169	5	4
β-strand	175-181	7	4
β-strand	184-185	2	4
β-strand	191-193	3	4
α-helix	197-211	15
α-helix	220-230	11
β-strand	233	1	5
α-helix	238-247	10
β-strand	254-259	6	6
β-strand	266-271	6	6
α-helix	274-277	4
α-helix	280-283	4
α-helix	285-287	3
α-helix	296-306	11
α-helix	309-317	9
β-strand	319-322	4	4
α-helix	324-326	3
β-strand	329	1	5
α-helix	331-354	24
α-helix	360-363	4
β-strand	367-368	2	4
α-helix	376-385	10
α-helix	388-391	4
α-helix	397-402	6
α-helix	405-409	5

Chain B: 17 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	8-13	6	7
β-strand	18-22	5	7
β-strand	30-32	3	7
β-strand	36	1	8
β-strand	71	1	8
β-strand	74-75	2	9
β-strand	78-79	2	9
α-helix	82-93	12
α-helix	102-104	3
β-strand	106-111	6	7
α-helix	117-125	9
α-helix	126-131	6
β-strand	135-140	6	7
α-helix	141-149	9
β-strand	154-159	6	10
β-strand	164-170	7	10
β-strand	173-174	2	10
β-strand	180-182	3	10
α-helix	186-199	14
α-helix	210-220	11
α-helix	227-236	10
β-strand	242-245	4	11
β-strand	251-254	4	11
α-helix	257-263	7
α-helix	268-271	4
α-helix	278-287	10
α-helix	291-299	9
β-strand	301-304	4	10
α-helix	306-308	3
α-helix	313-328	16
α-helix	335-337	3
β-strand	344-345	2	10
α-helix	353-364	12
β-strand	373	1	7
α-helix	375-378	4

Chain C: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	12
β-strand	14-16	3	13
β-strand	22-25	4	13
β-strand	32-38	7	13
β-strand	41-48	8	13
β-strand	55-61	7	14
β-strand	66-71	6	14
β-strand	76-82	7	14
β-strand	85-91	7	14
β-strand	99-104	6	14
β-strand	110-115	6	14
β-strand	120-126	7	14
β-strand	131-137	7	14
β-strand	145-150	6	15
β-strand	156-161	6	15
β-strand	166-170	5	15
α-helix	179-182	4
β-strand	183	1	16
β-strand	186	1	16
β-strand	194-198	5	15
β-strand	205-210	6	17
β-strand	216-221	6	17
β-strand	225-230	6	17
β-strand	236-241	6	17
α-helix	246	1
β-strand	247-252	6	18
β-strand	257-262	6	18
β-strand	268-273	6	18
β-strand	278-284	7	18
β-strand	329-336	8	12
β-strand	344-349	6	12
β-strand	353-358	6	12
α-helix	359-365	7

Chain D: 18 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	9-24	16
α-helix	26-30	5
β-strand	33-37	5	19
α-helix	38-40	3
β-strand	41-46	6	19
α-helix	48-50	3
β-strand	54-60	7	19
α-helix	64-68	5
α-helix	72-80	9
α-helix	81-83	3
β-strand	84-85	2	19
α-helix	86-88	3
β-strand	93-98	6	19
α-helix	106-114	9
α-helix	116-134	19
α-helix	139-141	3
β-strand	142-144	3	20
β-strand	151-156	6	20
β-strand	161-168	8	20
α-helix	172-186	15
α-helix	187-190	4
β-strand	197-202	6	20
α-helix	207-210	4
β-strand	220-227	8	20
α-helix	229-232	4
α-helix	234-244	11
α-helix	247-279	33

Chain E: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	14-16	3	21
β-strand	19-21	3	21
β-strand	24	1	22
α-helix	33	1
β-strand	34	1	22
α-helix	41-52	12
α-helix	64-82	19
α-helix	88-100	13
α-helix	103-105	3
α-helix	123-148	26
β-strand	149	1	23
β-strand	156	1	23
α-helix	158-161	4
α-helix	168-170	3

Chain F: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
α-helix	37-40	4
α-helix	44-46	3
β-strand	47	1	24
α-helix	48-50	3
β-strand	51-54	4	25
β-strand	60-65	6	25
β-strand	66	1	24
β-strand	69-74	6	25
α-helix	81-96	16
β-strand	104	1	25
α-helix	108-109	2
β-strand	114-119	6	25
α-helix	120-125	6
α-helix	128-166	39

Chain G: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	16-19	4
α-helix	39-47	9
α-helix	51-58	8
α-helix	69-85	17
α-helix	91-96	6
α-helix	100-114	15
α-helix	121-146	26

Chain H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	194-200	7
α-helix	203-206	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-related protein 3	A	protein	413	Bos taurus	P61157 (AlphaFold model)
Actin-related protein 2	B	protein	377	Bos taurus	A7MB62 (AlphaFold model)
Actin-related protein 2/3 complex subunit 1B	C	protein	372	Bos taurus	Q58CQ2 (AlphaFold model)
Actin-related protein 2/3 complex subunit 2	D	protein	300	Bos taurus	Q3MHR7 (AlphaFold model)
Actin-related protein 2/3 complex subunit 3	E	protein	178	Bos taurus	Q3T035
Actin-related protein 2/3 complex subunit 4	F	protein	168	Bos taurus	Q148J6
Actin-related protein 2/3 complex subunit 5	G	protein	143	Bos taurus	G3MXC8
Arpin	H	protein	34	Homo sapiens	Q7Z6K5

Sequence of entity 1 (A), FASTA

>7JPN_1 Actin-related protein 3 (chains A)
GRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFI
GDEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPEN
REYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAE
GYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEF
NKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDE
VIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKP
IDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFG

Sequence of entity 2 (B), FASTA

>7JPN_2 Actin-related protein 2 (chains B)
QGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDEASE
LRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNREKI
VEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTRRLD
IAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVLVES
YTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKHIVL
SGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAVLAD
IMKDKDNFWMTRQEYQE

Sequence of entity 3 (C), FASTA

>7JPN_3 Actin-related protein 2/3 complex subunit 1B (chains C)
MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGNKWVQVHELKEHNGQVTGIDW
APDSNRIVTCGTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNEKKFAVGSGSRVI
SICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNSVLLAAGSCDFKCRIFSAYIKEVEERP
APTPWGSKMPFGELMFESSSSCGWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATL
ASETLPLLAVTFITESSLVAAGHDCFPVLFTYDSAAGKLSFGGRLDVPKQSSQRGLTARE
RFQNLDKKASSEGSAAAGAGLDSLHKNSVSQISVLSGGKAKCSQFCTTGMDGGMSIWDVR
SLESALKDLKIV

Sequence of entity 4 (D), FASTA

>7JPN_4 Actin-related protein 2/3 complex subunit 2 (chains D)
MILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHISNPNGDKTKVMVSIS
LKFYKELQAHGADELLKRVYGSYLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNC
FASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKV
FMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTNASARDNT
INLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTITGKTFSSR

Sequence of entity 5 (E), FASTA

>7JPN_5 Actin-related protein 2/3 complex subunit 3 (chains E)
MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEI
KNEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKP
ANKQEDEVMRAYLQQLRQETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ

Sequence of entity 6 (F), FASTA

>7JPN_6 Actin-related protein 2/3 complex subunit 4 (chains F)
MTATLRPYLSAVRATLQAALCLENFSSQVVERHNKPEVEVRSSKELLLQPVTISRNEKEK
VLIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGYDISFLITN
FHTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKNF

Sequence of entity 7 (G), FASTA

>7JPN_7 Actin-related protein 2/3 complex subunit 5 (chains G)
ARFRKVDVDEYDENKFVDEEDGGDGQAGPDEGEVDSCLRQGNMTAALQAALKNPPINTKS
QAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSDNSSAVLLQW
HEKALAAGGVGSIVRVLTARKTV

Sequence of entity 8 (H), FASTA

>7JPN_8 Arpin (chains H)
ASWTDNIMAQKCSKGAAAEIREQGDGAEDEEWDD

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
MG	Magnesium ion	Mg	2

Primary citation

Molecular mechanism of Arp2/3 complex inhibition by Arpin. Fregoso, F.E., van Eeuwen, T., Simanov, G. et al. Nat Commun (2022) 13:628-628. DOI 10.1038/s41467-022-28112-2 · PubMed

Other PDB entries of the same protein (UniProt P61157 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1K8K 2.0 Å, Crystal Structure of Arp2/3 Complex
2P9I 2.46 Å, Crystal Structure of bovine Arp2/3 Complex co-crystallized with ADP and crosslinked with…
3UKR 2.48 Å, Crystal structure of Bos taurus Arp2/3 complex with bound inhibitor CK-666
3ULE 2.5 Å, Structure of Bos taurus Arp2/3 complex with bound inhibitor CK-869 and ATP
1TYQ 2.55 Å, Crystal structure of Arp2/3 complex with bound ATP and calcium
1U2V 2.55 Å, Crystal structure of Arp2/3 complex with bound ADP and calcium
2P9K 2.59 Å, Crystal structure of bovine Arp2/3 complex co-crystallized with ATP and crosslinked with…
2P9L 2.65 Å, Crystal Structure of bovine Arp2/3 complex
3RSE 2.65 Å, Structural and biochemical characterization of two binding sites for nucleation…
2P9S 2.68 Å, Structure of bovine Arp2/3 complex co-crystallized with ATP/Mg2+
3DXK 2.7 Å, Structure of Bos Taurus Arp2/3 Complex with Bound Inhibitor CK0944636
2P9U 2.75 Å, Crystal structure of bovine Arp2/3 complex co-crystallized with AMP-PNP and calcium

Browse structure collections

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